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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 1-100196274-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=100196274&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 100196274,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001918.5",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "c.1430T>G",
"hgvs_p": "p.Met477Arg",
"transcript": "NM_001918.5",
"protein_id": "NP_001909.4",
"transcript_support_level": null,
"aa_start": 477,
"aa_end": null,
"aa_length": 482,
"cds_start": 1430,
"cds_end": null,
"cds_length": 1449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000370132.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001918.5"
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "c.1430T>G",
"hgvs_p": "p.Met477Arg",
"transcript": "ENST00000370132.8",
"protein_id": "ENSP00000359151.3",
"transcript_support_level": 1,
"aa_start": 477,
"aa_end": null,
"aa_length": 482,
"cds_start": 1430,
"cds_end": null,
"cds_length": 1449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001918.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370132.8"
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "c.1556T>G",
"hgvs_p": "p.Met519Arg",
"transcript": "ENST00000681617.1",
"protein_id": "ENSP00000505544.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 524,
"cds_start": 1556,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000681617.1"
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "c.1430T>G",
"hgvs_p": "p.Met477Arg",
"transcript": "ENST00000875462.1",
"protein_id": "ENSP00000545521.1",
"transcript_support_level": null,
"aa_start": 477,
"aa_end": null,
"aa_length": 482,
"cds_start": 1430,
"cds_end": null,
"cds_length": 1449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875462.1"
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "c.1358T>G",
"hgvs_p": "p.Met453Arg",
"transcript": "ENST00000875463.1",
"protein_id": "ENSP00000545522.1",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 458,
"cds_start": 1358,
"cds_end": null,
"cds_length": 1377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875463.1"
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "c.1352T>G",
"hgvs_p": "p.Met451Arg",
"transcript": "ENST00000948414.1",
"protein_id": "ENSP00000618473.1",
"transcript_support_level": null,
"aa_start": 451,
"aa_end": null,
"aa_length": 456,
"cds_start": 1352,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948414.1"
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "c.1238T>G",
"hgvs_p": "p.Met413Arg",
"transcript": "ENST00000875464.1",
"protein_id": "ENSP00000545523.1",
"transcript_support_level": null,
"aa_start": 413,
"aa_end": null,
"aa_length": 418,
"cds_start": 1238,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875464.1"
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "c.1088T>G",
"hgvs_p": "p.Met363Arg",
"transcript": "ENST00000875465.1",
"protein_id": "ENSP00000545524.1",
"transcript_support_level": null,
"aa_start": 363,
"aa_end": null,
"aa_length": 368,
"cds_start": 1088,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875465.1"
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "c.887T>G",
"hgvs_p": "p.Met296Arg",
"transcript": "NM_001399969.1",
"protein_id": "NP_001386898.1",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 301,
"cds_start": 887,
"cds_end": null,
"cds_length": 906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001399969.1"
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "c.887T>G",
"hgvs_p": "p.Met296Arg",
"transcript": "NM_001399972.1",
"protein_id": "NP_001386901.1",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 301,
"cds_start": 887,
"cds_end": null,
"cds_length": 906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001399972.1"
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "c.887T>G",
"hgvs_p": "p.Met296Arg",
"transcript": "ENST00000681780.1",
"protein_id": "ENSP00000505780.1",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 301,
"cds_start": 887,
"cds_end": null,
"cds_length": 906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000681780.1"
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "c.887T>G",
"hgvs_p": "p.Met296Arg",
"transcript": "XM_017000468.3",
"protein_id": "XP_016855957.1",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 301,
"cds_start": 887,
"cds_end": null,
"cds_length": 906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000468.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "n.1262T>G",
"hgvs_p": null,
"transcript": "NR_174363.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_174363.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "n.1603T>G",
"hgvs_p": null,
"transcript": "NR_174364.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_174364.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "n.1227T>G",
"hgvs_p": null,
"transcript": "NR_174365.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_174365.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"hgvs_c": "n.1529T>G",
"hgvs_p": null,
"transcript": "NR_174366.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_174366.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285530",
"gene_hgnc_id": null,
"hgvs_c": "n.140-22370A>C",
"hgvs_p": null,
"transcript": "ENST00000835180.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000835180.1"
}
],
"gene_symbol": "DBT",
"gene_hgnc_id": 2698,
"dbsnp": "rs398123662",
"frequency_reference_population": 0.0000030980855,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000273631,
"gnomad_genomes_af": 0.00000657557,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9617688655853271,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.735,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9686,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.19,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.947,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001918.5",
"gene_symbol": "DBT",
"hgnc_id": 2698,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1430T>G",
"hgvs_p": "p.Met477Arg"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000835180.1",
"gene_symbol": "ENSG00000285530",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.140-22370A>C",
"hgvs_p": null
}
],
"clinvar_disease": "Maple syrup urine disease,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:2 US:1",
"phenotype_combined": "not provided|Maple syrup urine disease",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}